Several of them are somehow converted into school children drop off zones for cars during the morning (i.e., at the time that people should be commuting on them they're made even more dangerous - Des Plaines Ave near the church school for example) And of course despite multiple calls out to advocacy groups and local leadership, nothing seems to beat the "for the children" argument, despite the fact that what it's really doing is "for the traffic" more than anything.
That's one of many examples though, but the short of it is - things like protected bike lanes ignore the real problems in urban commuting, of which there are essentially four, in my opinion:
1 - Traffic is too fast - The basic speed limit unless posted otherwise, in the city of Chicago is 30mph. this speed limit is nearly NEVER enforced by police (Hello free revenue stream?) and traffic down major streets regularly goes at 50+ mph.
2 - Traffic is too slow - congested streets cause just as many problems as speeding. Being in a car when you're stuck in stop light to stop light traffic is infuriating. People are constantly looking for a move they can make to avoid it. Even with a bike lane, cars will constantly try to pass on the right, use what's supposed to be parking to make moves towards turning early, etc. This has been the source of my own collisions with automobiles 4/5 times I've had them in 10 years.
3 - Lack of a safe place to stow the bike. Any respectable bike will cost $500.00 and up. Sure, you can get some used single speed or old ten speed for less, but walk into any shop, and you won't see much below that. Locking those outside, especially on a regular schedule, makes them not last very long. (not to mention weather, which while often fine to do a short ride in, all day exposed to can wreak havoc on even a great bike).
4 - The whole, stinky at work, work stigma, aging building infrastructure problem. Sure, a few downtown offices have showers, but it's certainly the exception (spoken as a developer who's worked in many offices over the years) and in some companies being "that guy" seems to have it's own negative connotations.
Want to spend that bike-focused infrastructure money well? Start offering tax breaks to companies providing showers (I'd hear this was a thing once, but never found any proof of it), or safe places to store bicycles indoors. Want to create more of that bike-focused infrastructure money? Start enforcing speed limit laws that exist already, and start looking more towards traffic patterns for cars as a whole, and stick to shared lanes and painted lanes.